Dear Ed,
We wouldn't recommend doing it this way.
Instead we would register the FLAIR to a T1 image of the same subject with a linear (6 DOF) registration and then do a non-linear registration of the T1w image of that subject to the MNI T1 template, and finally combine the two registrations. This last step is easily done with either applywarp (for getting a resampled image) or convertwarp (for getting a combined warpfield).
All the best,
Mark
On 26 Jul 2012, at 11:59, Ed Gronenschild wrote:
> Hi,
>
> What is the correct use of options to fsl_reg to non-linear register
> a FLAIR volume onto the MNI T1 template (called ch2 in MRICRON)?
> In particular which fnirt options (config) should I supply?
>
> Cheers,
> Ed
>
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